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Old 01-03-2011, 11:47 PM   #1
Yushan Hsiao
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Location: Taiwan

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Default Any tools for RNA graph?

I need to draw the secondary structure of small RNA precursors.
Is there any tool that could produce many graphs at a time when I give it the all the sequences or parenthesis of RNAfold?

Besides, I also want to mark the specific sequence on the graph of my RNA structure. I saw some paper with red letters on the graph to point them out, but I don't know how do they produce this result?

Could anyone help? Thanks a lot.
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Old 01-04-2011, 01:24 AM   #2
ppgardne
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Default

VARNA is quite good. Lots of different layouts are possible.

The Vienna package ships with RNAplot which will ps & svg. RNAfold usually generates a postscript (rna.ps) by default. There are some scripts for manipulating the Vienna ps files in your ViennaRNA-1.x.x/Utils/ directory.
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Old 01-10-2011, 01:04 AM   #3
ppgardne
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R2R has just been published. It also produces some very nice graphics:
http://www.biomedcentral.com/1471-2105/12/3
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